Taxonomy is the science of classifying plants, animals, and microorganisms into increasingly broader categories based on shared features. Traditionally, organisms were grouped by physical resemblances, but in recent times other criteria such as genetic matching have also been used. Scientific naming of species emerged in the 1600s, the Swedish naturalist Carl Linnaeus then put it all together in the 1700s. It ended up with seven categories from least specific to most specific (Figure 10-01a, left diagram). An organism's name is designated with entry from the categories of Genus and Species (in Latin). For example, human belongs to the genus Homo (in capital) and the species sapiens - hence Homo sapiens (in italic). However, such naming system is not perfect; it has incited many heated debates among taxonomists for the assignment of organism into certain category. The confusion led to new concepts

such as the phylogenetic species, which emphasizes shared traits from common ancestor (Figure 10-01a, right diagram). Another scheme involves comparing DNA sequences as shown in Figure 01-02a.

A detailed documentation for all species of life on Earth can be found in the "Encyclopedia Of Life" website.

Biology used to classify living organisms into five kingdoms as shown in Figure 10-01b. They include prokaryotes (no nucleus, no organelles), protista (possess nucleus and organelles), fungi, plants, and animals. The time scale (in billions of years) is referred to the appearance of oldest fossils. Study of DNA variation among different species provides another way to classify them as shown by the tree of life in Figure 10-02a. According to this scheme the common ancestor at the base of the tree gave rise to three branches:

microbes known as archaea (primitive unicellular organisms that live in most extreme environments), bacteria (unicellular organisms without nucleus or cell structure), and eukaryotes (any organism with one or more cells that have visible nucleus and organelles). The lengths of the branches reflect how much the DNA of each lineage has diverged from their common ancestor. They demonstrate that most of life's genetic diversity turns out to be microbial; the entire animal kingdom (shown at the upper right) are just a few twigs at one end of the tree. It is obvious that multicellular organisms such as fungi, plants and animals evolved from unicellular organisms further down the tree. Figure 10-02b expresses pictorally the same kind of division including a hypothetical "Mother of all life" at the very bottom - the "last universal common ancestor" (LUCA).

Recently, new evidence suggests that the Tree of Life may be more complicated than the version shown in Figure 10-02a. The revised version indicates that early life may not have existed as distinct species; instead they may have traded their genes promiscuously. Life may descend from a huge primordial menagerie rather than from a single common ancestor. Billions of years later, after the three branches split apart, distantly related species still joined together sometimes, as bacteria were swallowed up by other organisms.

Two of these fusions - bacteria giving rise to mitochondria and chloroplasts - are shown in the new Tree of Life (Figure 10-02c). In view of such common

practices of lateral gene transfer and endosymbiosis, it is proposed in 2004 that the the tree of life should be replaced by the ring of life as shown in Figure 10-02d. In this diagram, the eukaryotes is the product of the fusion of genomes between some type of archaea with some type of bacteria. The eukaryotic root organisms comprise the eukaryotic realm on the left-hand side. Ancestors defining major groups in the prokaryotic realm are indicated by small circles on the ring. The archaea, shown on the right, includes the euryarchaea, and the eocyta.

The time scale derived from fossil records is usually calculated from radioactive dating. For example in carbon-14 dating, the fact that the ratio of C14 to C12 is fairly constant (~ 10-12) in living organisms and that C14 is radioactive with a halflife of about 5730 years, would yield the age of the organism since its death (no more accumulation of C14) if we measure the leftover amount of C14 in the sample (See more detail on Dating-Radioactive). The DNA variation (between species) shows only the genetic difference, which can be calibrated with known time difference from fossil records (Figure 10-02e).

However, this calibration can be extrapolated to the unknown region only if the rate of DNA base substitution (the molecular clock) is constant. Unfortunately, it is found that genes change (mutate) at different rates.

Another method for determining the relationship between organisms is to check the number of replacements within the amino acid sequence of certain protein. Presumably, fewer replacements correspond to closer relationship. Figure 10-02f presents the number of replacements between

human, monkey, and horse in the cytochrome-c protein. Each letter represents an aminoacid, and a dot indicates the same amino acid as in humans. Figure 10-02g shows the phy-logeny of 20 organisms (including fungi, and many kinds of animals), based on differences in the amino acid sequence of cytochrome-c. The fractional numbers are calculated to best-fit the data with imaginary splitting

Figure 10-02g Phylogeny

points. It corresponds fairly well to the relationships determined from other sources, such as the fossil record.

Cytochrome-c is an electron transporting protein that resides within the inter-membrane space of the mitochondria, where it plays a critical role in the process of oxidative phosphorylation and production of cellular ATP. An increasing amount of interest has been directed toward the role which cytocrome C has been demonstrated to play in apoptotic processes. It consists of 104 amino acids, encoded by 312 nucleotides. Cytochrome-c is a slowly evolving protein. Widely different species have in common a large proportion of the amino acids in their cytochrome-c, which makes possible the study of genetic differences between organisms only remotely related. Other proteins, such as the hemoglobin that evolves more rapidly than cytochrome-c, can be studied in order to establish phylogenictic relationships between closely related species as shown in Figure 10-02h, which also calibrates the time scale of amino acid change for the various proteins.